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Horse liver L57F alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)
METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA,
10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL
ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.5 α = 91.8 b = 51.52 β = 103.07 c = 92.54 γ = 110.42
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS 2007-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.09 19.89 88 0.103 0.113 10 5.52 273671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.13 50.2 0.242 0.285 3.4 3.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DWV 1.1 19.9 267504 2639 89.28 0.1184 0.1183 0.1182 0.1324 0.1325 RANDOM 15.169
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.27 -0.77 0.19 0.63 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.788 r_dihedral_angle_1_deg 17.649 r_dihedral_angle_4_deg 16.422 r_dihedral_angle_3_deg 11.187 r_rigid_bond_restr 2.327 r_angle_refined_deg 1.836 r_angle_other_deg 1.541 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.788 r_dihedral_angle_1_deg 17.649 r_dihedral_angle_4_deg 16.422 r_dihedral_angle_3_deg 11.187 r_rigid_bond_restr 2.327 r_angle_refined_deg 1.836 r_angle_other_deg 1.541 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5576 Nucleic Acid Atoms Solvent Atoms 1138 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling PDB_EXTRACT data extraction d*TREK data reduction REFMAC phasing